Molecular Ecology

Many habitats on the planet are threatened by human development and shifts in climate, but some local populations are showing signs of resistance to stress. Both acclimation and adaptation have been implicated in this resistance, especially among populations with variation in traits critical for survival. This phenotypic variation can arise through genetic variation, environmental variation and the interaction of genotype and environment. However, we don’t know the amount of variation in organisms and whether there is enough standing variation to ensure the survival of many species.

The molecular ecology aspect of my research has been developed to better understand evolution and conservation at a time when many organisms face unprecedented stressors. I test how existing phenotypic variation in corals might allow them to persist in a changing world. Understanding how corals respond to both local and global scale stressors is critical to ensuring that these ecosystem engineers persist, especially since they provide habitat for a huge diversity of creatures and important ecosystem services for humans. Even though corals are susceptible to warming oceans (coral bleaching) there maybe enough variation in thermal resistance that will allow some genotypes to persist.

My dissertation research focused on using molecular techniques to better understand the patterns of genotypic diversity in corals of Hawaii. Specifically I’m interested in the distribution and diversity of genotypes and whether different genotypes of corals can tolerate different amounts and types of stress. Even though this question is basic to the ecology, evolution and conservation of these habitat-building animals, very little is known about the diversity of responses to stress in corals. This is especially important in Hawai’i where local stressors (land development, invasive species and overfishing) might be interacting with global (warming seawater temperatures and ocean acidification) stressors to threaten coral persistence.

In 2014 and 2015 there was a coral bleaching event on the Hawaiian Islands. I surveyed the extent of bleaching in Kaneohe Bay, and have been monitoring 200 individual corals found in pairs of a bleached next to a healthy colony. These corals are monitored for health with monthly photographs and are surveyed on regular intervals to track type and abundance of zooxanthellae using qPCR. This work is ongoing and includes monitoring physical parameters (light, temperature, sedimentation rates, and salinity) at 6 sites throughout Kaneohe Bay.

Using next generation sequencing (NGS) techniques we have the tools to test whether different populations of corals can acclimate or adapt to modern stressors. Gene regulation is one mechanism that eukaryotes use to respond to stress and more than 20,000 genes can be monitored for their expression levels using the NGS technique RNAseq. I am testing the potential for acclimation between corals that are bleaching and those that remain healthy. This transcriptome will help us understand how corals respond to stress, and what some corals might do differently to resist thermal stress. I am currently sequencing the transcriptome of bleached and healthy corals. I am assembling this transcriptome using bioinformatics and the program Trinity. With this transcriptome I’ll be able to measure which genes are up and down regulated in corals that are bleached compared to their healthy neighbor.

Adaptation is a potential long term mechanism for corals to cope with climate change. Already within populations we see phenotypic and corresponding genotypic diversity. The underlying genetic richness and variation of a population is an important aspect of evolution to changing environments. The potential for coral adaptation is a population genetics question. Some corals contain mutations (SNPs) in their genome that confer a selective advantage to some individuals within a population. The NGS technique RAD sequencing has improved our ability to detect these SNPs, and with replicated samples can identify over 20,000 mutations. A variation of RAD (ezRAD) was used on the paired corals from Kaneohe Bay. The data for 16 pairs of Porites compressa produced over 32 GBS of sequence data. Using dDocent and VCF tools over 47,000 variant sites were identified. Using the program PCAdapt P. compressa were found to be two cryptic clades, suggesting there is unidentified diversity within this coral species. These data continue to be analyzed and will inform researchers and managers about the genetic diversity of corals on their reefs and will provide an important baseline to track changing diversity during climate change events.

Corals build coral reefs and provide critical habitat for millions of species, but they are very susceptible to changing climate. Even though I use techniques that could be applied to any organism, I have focused my recent research on corals because of the pressing need for their conservation. We must understand how corals respond to stress and how they can adapt to it before we can manage our reefs for persistence.